The complete coding sequence of preapolipoprotein C-II has been determined from an apoC-II clone isolated from a normal human liver cDNA library. PreapoC-II contains a 22 amino acid signal peptide attached to the 79 amino acid mature protein. This is similar to other secretory proteins that are synthesized as precursors and undergo subsequent modification. In collaboration with A.Y. Sakaguchi and associates, we have localized the apoC-II gene to chromosome 19. Analysis of the apoC-II gene in apoC-II deficiency was done by hybridization following Southern blotting of genomic DNA from 2 independent patients with apoC-II deficiency. The apoC-II gene is present in these patients with no major insertions or deletions. Analysis of the plasma in the apoC-II deficient patients by 2 dimensional gel electrophoresis and Western blotting revealed the presence of apoC-II variants with abnormal electrophoretic mobility. Family studies suggests that the proband from one of the apoC-II deficient families is a compound heterozygote.